|
| Status |
Public on Jun 01, 2019 |
| Title |
ATAC-seq EB WT re2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Trim33 WT
strain: C57Bl/6J background ESCs(Xi et al., 2011)
cell type: d2.5 EBs
|
| Treatment protocol |
Trim33 WT ESCs in C57Bl/6J background were cultured on ultra-low plates withdraw LIF and cells were harvested at d2.5
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).
|
| Growth protocol |
Trim33 WT ESCs in C57Bl/6J background were cultured on ultra-low plates withdraw LIF and medium were changed every two days, cells were harvested at d2.5
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After dissociation with Trypsin, embryonic stem cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using STAR version 2.4.0, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.2.1
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Jun 01, 2019 |
| Contact name |
Bofeng Liu |
| E-mail(s) |
lbf12thu@gmail.com
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Science
|
| Lab |
Xie Wei Lab
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE115169 |
Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33 |
|
| Relations |
| BioSample |
SAMN09289126 |
| SRA |
SRX4147804 |
